Comparative Analysis of GRAS Genes in Six Cucurbitaceae Species Provides Insights into Their Evolution and Function

Round 1

Reviewer 1 Report

A brief explanation of each section of the report is given below;

Title: It is adequate for the content, informative, concise, and clear.

Abstract: It is comprehensive by itself. All the important and essential information of the article is included. Structure and length: The overall structure of the article well organized and well balanced. The article is written with the minimum length necessary for all relevant information.
Logic: The article written clearly and correctly. It is logically consistent. Figures and tables: They essential and clearly presented. English: English used in the article is very good. Scientific quality rating: The article is novel and original. The article contains material that is new or adds significantly to knowledge already published. Importance and impact: The presented results are of significant importance and impact to advancement in the relevant field of research. References: Appropriate and adequate references to related works covered sufficiently in the list. Incorporate some latest references. The article should become acceptable in its present form.

Author Response

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Reviewer 2 Report

This manuscript focus on the comparative study of GRAS genes in six Cucurbitaceae species to get insights on their evolution and function. In general, study is novel and provides new information about GRAS genes for genetic research and their association with agronomic traits of six cucurbits. In my opinion, abstract, introduction, M&M, result, discussion and conclusion is presented well and this manuscript can be accepted in this form with spelling correction of ‘ripening’ at line 447.

Author Response

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Reviewer 3 Report

The manuscript from a methodological point of view is mostly correct. Material & Method, Results and Discussion sections require improvement. I list some but not limited errors here:

General comment:  Check carefully text and correct minor errors e.g. in line 44 is only abbreviation DLT without expanding of this abbreviation, in line 47 ‘gran size’ should be replaced with ‘grain size’.

 

Figure 4b: I assume that the "DAPs" under the graphs refer to fruit stages, e.g. DAP10 it means fruit obtained 10 days after pollination. What does ‘DAFs’ mean? It is only mistake? Figure 4b should be better described.

 

Lines 169-174: Add information about maintaining light conditions during tissue preparation experiment for RT-qPCR analysis.  What was the intensity of the light if you write “normal light conditions”. How your light conditions correspond with light conditions maintaining during RNAseq experiment (weak light and high light conditions).

 

Lines 338-394 and relevant part in the discussion: This text is debatable than describing your own results. I don't exactly understand the authors' use of publicly available RNAseq data as the results from which the authors draw assumptions. Especially since the RNAseq data has not been verified by qPCR.

 

Lines 361-368 in the Results and Figure 5b and relevant part in the discussion: You wrote: “Our results revealed that Csa1P408720 and its homologous genes from five other cucurbit crops were located in the DELLA-2 clades and exhibited an ascending trend under dark treatment”.  And then [...] “The findings of this study suggest that these DELLA-2 genes may participate in the reaction to dark conditions during hypocotyl elongation and potentially function as a protective mechanism against hypocotyl overgrowth in cucurbit crops”

I think this is an over-interpretation because this trend is only confirmed in cucumber, melon and wax gourd. In other species this trend is not statistically significant, if I understand correctly. In text under Figure 5b you wrote: ‘The statistical significance of the differences was indicated by asterisks (P < 0.05)’.  Only three genes (Csa1P408720, MELO3C025288 and Bhi02P000894) fulfils this requirement. For the other three genes p-value ranges from 0.27 to 0.43, so this results are not statistically significant. Besides, the asterisks were not marked on the chart.

Lines 482-483: In my opinion RNAseq data and qPCR do not provide evidence to form such conclusions ‘Additionally, we found evidence of GRAS genes involved in regulating hypocotyl elongation under weak or dark light conditions’.

Author Response

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Reviewer 4 Report

Comments:

In the present study entitled “Comparative analysis of GRAS genes in six Cucurbitaceae species provides insights into their evolution and function”, authors have systematically identified and characterized the GRAS genes in cucurbitaceous species which emphasized their biological functions and evolutionary patterns over the speciation. The study is quite interesting to relate the GRAS gene evolution and classification in cucurbits. The investigations are also technical sound too. However, some pitfalls are observed which can be rectified to improve the manuscript for global readability and acceptance.  The language of the manuscript is quite good. The comments observed during review of the manuscripts are as follows:

General comments:

The following general comments related to language, typological errors, etc. are mentioned as bellow: -

Comment #1 – Check space between the words and phrases. For example between ‘[8, 9]and’ at line number 41, ‘[13, 14]hormone-’ at line number 46, and so on.

Comment #2 – Authors should short and bi-furcate the sentence “DELLAs, which belong …………. with multiple regulatory proteins [6, 28]” at line number 59-64.

 Comment #3 – The manuscript should be checked carefully again. The typological error and fond styles are not uniform at various places in the text of manuscript. The name of Arabidopsis should be italicized in the whole document of manuscript.

 

Scientific comments:

Comment #1 – Authors have stated that “The genome sequences, protein sequences, and annotation information were obtained” but not mentioned the resource database at line number 84-86.

Comment #2 – Authors must mention the reaction and thermo-cycling conditions adopted during qRT-PCR assay in this study at line number 181-183.

Comment #3 – Authors have replicated the experiment thrice but not mentioned the statistical analysis which used to calculate standard errors among the replicates at line number 185.

Comment #4 – Authors have just mentioned the ‘GRAS members; instead of mentioning ‘GRAS gene family members’ at line number 194.

Comment #5 – If possible, the results related to Cis-acting elements, can be presented in the graphical representation.

Author Response

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Round 2

Reviewer 3 Report

The authors responded in detail to my comments and questions and corrected any misunderstandings. The presented manuscript is ready for publication.